2WJQ - JenaLib

Title :   NANC PORIN STRUCTURE IN HEXAGONAL CRYSTAL FORM.

Authors :   C. Wirth, G. Condemine, T. Schirmer, C. M. Peneff

Date :   28 May 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A

Keywords :   Kdgm Family, Beta-Barrel, Monomeric Porin, Transport Protein, Outer Membrane Protein, Sialic Acid Translocation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Wirth, G. Condemine, C. Boiteux, S. Berneche, T. Schirmer, C. M. Peneff
Nanc Crystal Structure, A Model For Outer Membrane Channels Of The Acidic Sugar-Specific Kdgm Porin Family.
J. Mol. Biol. V. 394 718 2009
PubMed-ID: 19796645 | Reference-DOI: 10.1016/J.JMB.2009.09.054

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (14, 14)

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:81 , TRP A:110 , ARG A:124 , ASN A:126 , HOH A:2102	BINDING SITE FOR RESIDUE CL A1216
02	AC2	SOFTWARE	ARG A:158 , LYS A:164	BINDING SITE FOR RESIDUE CL A1217
03	AC3	SOFTWARE	VAL A:5	BINDING SITE FOR RESIDUE OCT A1218
04	AC4	SOFTWARE	TYR A:16 , TYR A:175 , LDA A:1227	BINDING SITE FOR RESIDUE OCT A1220
05	AC5	SOFTWARE	TRP A:146 , THR A:148 , ASN A:169	BINDING SITE FOR RESIDUE OCT A1230
06	AC6	SOFTWARE	TYR A:207	BINDING SITE FOR RESIDUE OCT A1221
07	AC7	SOFTWARE	OCT A:1225	BINDING SITE FOR RESIDUE OCT A1222
08	AC8	SOFTWARE	LEU A:65 , ASP A:66 , OCT A:1224	BINDING SITE FOR RESIDUE OCT A1223
09	AC9	SOFTWARE	OCT A:1223	BINDING SITE FOR RESIDUE OCT A1224
10	BC1	SOFTWARE	TRP A:146 , TYR A:189 , OCT A:1222	BINDING SITE FOR RESIDUE OCT A1225
11	BC2	SOFTWARE	TYR A:106	BINDING SITE FOR RESIDUE LDA A1226
12	BC3	SOFTWARE	TYR A:16 , THR A:18 , ASN A:40 , THR A:178 , TYR A:207 , OCT A:1220	BINDING SITE FOR RESIDUE LDA A1227
13	BC4	SOFTWARE	GLN A:68 , ALA A:96 , ILE A:104 , GLY A:132 , TRP A:165 , LDA A:1229	BINDING SITE FOR RESIDUE LDA A1228
14	BC5	SOFTWARE	ILE A:104 , TRP A:130 , SER A:152 , LDA A:1228 , HOH A:2045	BINDING SITE FOR RESIDUE LDA A1229

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:205
 aligned with NANC_ECOLI | P69856 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:215
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     
           NANC_ECOLI    24 ATLDVRGGYRSGSHAYETRLKVSEGWQNGWWASMESNTWNTIHDNKKENAALNDVQVEVNYAIKLDDQWTVRPGMLTHFSSNGTRYGPYVKLSWDATKDLNFGIRYRYDWKAYRQQDLSGDMSRDNVHRWDGYVTYHINSDFTFAWQTTLYSKQNDYRYANHKKWATENAFVLQYHMTPDITPYIEYDYLDRQGVYNGRDNLSENSYRIGVSFKL 238
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wjqA00 A:1-215 Oligogalacturonate-specifi          c porin protein (KdgM)                                                                                                                                              CATH domains
               Pfam domains KdgM-2wjqA01 A:1-215                                                                                                                                                                                                    Pfam domains
         Sec.struct. author .eeeeeeeee....eeeeeeeeeee....eeeeeeeeeeee.----------.eeeeeeee.......eeeeeeeeeeee..eeeeeeeeeeeee....eeeeeeeeeeee...ee.....ee...eeeeeeeeeee....eeeeeeeeeeee...........eeeeeeeeeee.....eeeeeeeee....eee..eeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wjq A   1 ATLDVRGGYRSGSHAYETRLKVSEGWQNGWWASMESNTWNTI----------NDVQVEVNYAIKLDDQWTVRPGMLTHFSSNGTRYGPYVKLSWDATKDLNFGIRYRYDWKAYRQQDLSGDMSRDNVHRWDGYVTYHINSDFTFAWQTTLYSKQNDYRYANHKKWATENAFVLQYHMTPDITPYIEYDYLDRQGVYNGRDNLSENSYRIGVSFKL 215
                                    10        20        30        40 |       -  |     60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     
                                                                    42         53

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (NANC_ECOLI | P69856)

molecular function
	GO:0015478	oligosaccharide transporting porin activity	Catalysis of the transfer of oligosaccharide, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
	GO:0015136	sialic acid transmembrane transporter activity	Enables the transfer of sialic acid from one side of the membrane to the other.
biological process
	GO:1901264	carbohydrate derivative transport	The directed movement of a carbohydrate derivative into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0008643	carbohydrate transport	The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are any of a group of organic compounds based of the general formula Cx(H2O)y.
	GO:1905039	carboxylic acid transmembrane transport	The directed movement of carboxylic acid across a membrane.
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015772	oligosaccharide transport	The directed movement of oligosaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligosaccharides are molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0045203	integral component of cell outer membrane	The component of the cell outer membrane consisting of the gene products having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

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